Starting phenix.real_space_refine on Mon May 26 18:55:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbh_27284/05_2025/8dbh_27284.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbh_27284/05_2025/8dbh_27284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dbh_27284/05_2025/8dbh_27284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbh_27284/05_2025/8dbh_27284.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbh_27284/05_2025/8dbh_27284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbh_27284/05_2025/8dbh_27284.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.397 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 60 5.49 5 Mg 24 5.21 5 S 204 5.16 5 C 17904 2.51 5 N 5040 2.21 5 O 5652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 204 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28884 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "E" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "F" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "G" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "H" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "I" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "J" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "K" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "L" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 636 residue: pdb=" N HIS A 12 " occ=0.58 ... (8 atoms not shown) pdb=" NE2 HIS A 12 " occ=0.58 residue: pdb=" N ARG A 22 " occ=0.80 ... (9 atoms not shown) pdb=" NH2 ARG A 22 " occ=0.80 residue: pdb=" N GLU A 26 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 26 " occ=0.40 residue: pdb=" N LYS A 29 " occ=0.40 ... (7 atoms not shown) pdb=" NZ LYS A 29 " occ=0.40 residue: pdb=" N LYS A 33 " occ=0.01 ... (7 atoms not shown) pdb=" NZ LYS A 33 " occ=0.01 residue: pdb=" N SER A 36 " occ=0.01 ... (4 atoms not shown) pdb=" OG SER A 36 " occ=0.01 residue: pdb=" N ASN A 37 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN A 37 " occ=0.50 residue: pdb=" N CYS A 41 " occ=0.89 ... (4 atoms not shown) pdb=" SG CYS A 41 " occ=0.89 residue: pdb=" N GLU A 43 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 43 " occ=0.40 residue: pdb=" N GLU A 46 " occ=0.88 ... (7 atoms not shown) pdb=" OE2 GLU A 46 " occ=0.88 residue: pdb=" N SER A 58 " occ=0.10 ... (4 atoms not shown) pdb=" OG SER A 58 " occ=0.10 residue: pdb=" N GLY A 59 " occ=0.01 ... (2 atoms not shown) pdb=" O GLY A 59 " occ=0.01 ... (remaining 624 not shown) Time building chain proxies: 15.60, per 1000 atoms: 0.54 Number of scatterers: 28884 At special positions: 0 Unit cell: (126.531, 138.109, 139.763, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 204 16.00 P 60 15.00 Mg 24 11.99 O 5652 8.00 N 5040 7.00 C 17904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.32 Conformation dependent library (CDL) restraints added in 3.5 seconds 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7008 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 36 sheets defined 44.0% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 62 through 80 Processing helix chain 'A' and resid 107 through 120 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 226 through 239 Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER A 314 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 Processing helix chain 'B' and resid 62 through 80 Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 226 through 239 Processing helix chain 'B' and resid 256 through 264 Processing helix chain 'B' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER B 314 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 62 through 80 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 161 through 164 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 226 through 239 Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 306 Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER C 314 " --> pdb=" O TYR C 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 Processing helix chain 'D' and resid 62 through 80 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 131 through 138 Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 161 through 164 Processing helix chain 'D' and resid 174 through 186 Processing helix chain 'D' and resid 226 through 239 Processing helix chain 'D' and resid 256 through 264 Processing helix chain 'D' and resid 277 through 284 removed outlier: 3.668A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 306 Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.631A pdb=" N SER D 314 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 24 Processing helix chain 'E' and resid 62 through 80 Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 131 through 138 Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 161 through 164 Processing helix chain 'E' and resid 174 through 186 Processing helix chain 'E' and resid 226 through 239 Processing helix chain 'E' and resid 256 through 264 Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.668A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 306 Processing helix chain 'E' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER E 314 " --> pdb=" O TYR E 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 24 Processing helix chain 'F' and resid 62 through 80 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 131 through 138 Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 161 through 164 Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 226 through 239 Processing helix chain 'F' and resid 256 through 264 Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 306 Processing helix chain 'F' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER F 314 " --> pdb=" O TYR F 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 62 through 80 Processing helix chain 'G' and resid 107 through 120 Processing helix chain 'G' and resid 131 through 138 Processing helix chain 'G' and resid 147 through 159 Processing helix chain 'G' and resid 161 through 164 Processing helix chain 'G' and resid 174 through 186 Processing helix chain 'G' and resid 226 through 239 Processing helix chain 'G' and resid 256 through 264 Processing helix chain 'G' and resid 277 through 284 removed outlier: 3.668A pdb=" N HIS G 283 " --> pdb=" O ASP G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 306 Processing helix chain 'G' and resid 309 through 314 removed outlier: 3.631A pdb=" N SER G 314 " --> pdb=" O TYR G 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 24 Processing helix chain 'H' and resid 62 through 80 Processing helix chain 'H' and resid 107 through 120 Processing helix chain 'H' and resid 131 through 138 Processing helix chain 'H' and resid 147 through 159 Processing helix chain 'H' and resid 161 through 164 Processing helix chain 'H' and resid 174 through 186 Processing helix chain 'H' and resid 226 through 239 Processing helix chain 'H' and resid 256 through 264 Processing helix chain 'H' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS H 283 " --> pdb=" O ASP H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 306 Processing helix chain 'H' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER H 314 " --> pdb=" O TYR H 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 24 Processing helix chain 'I' and resid 62 through 80 Processing helix chain 'I' and resid 107 through 120 Processing helix chain 'I' and resid 131 through 138 Processing helix chain 'I' and resid 147 through 159 Processing helix chain 'I' and resid 161 through 164 Processing helix chain 'I' and resid 174 through 186 Processing helix chain 'I' and resid 226 through 239 Processing helix chain 'I' and resid 256 through 264 Processing helix chain 'I' and resid 277 through 284 removed outlier: 3.668A pdb=" N HIS I 283 " --> pdb=" O ASP I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 292 through 306 Processing helix chain 'I' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER I 314 " --> pdb=" O TYR I 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 24 Processing helix chain 'J' and resid 62 through 80 Processing helix chain 'J' and resid 107 through 120 Processing helix chain 'J' and resid 131 through 138 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 161 through 164 Processing helix chain 'J' and resid 174 through 186 Processing helix chain 'J' and resid 226 through 239 Processing helix chain 'J' and resid 256 through 264 Processing helix chain 'J' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS J 283 " --> pdb=" O ASP J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 306 Processing helix chain 'J' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER J 314 " --> pdb=" O TYR J 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 24 Processing helix chain 'K' and resid 62 through 80 Processing helix chain 'K' and resid 107 through 120 Processing helix chain 'K' and resid 131 through 138 Processing helix chain 'K' and resid 147 through 159 Processing helix chain 'K' and resid 161 through 164 Processing helix chain 'K' and resid 174 through 186 Processing helix chain 'K' and resid 226 through 239 Processing helix chain 'K' and resid 256 through 264 Processing helix chain 'K' and resid 277 through 284 removed outlier: 3.668A pdb=" N HIS K 283 " --> pdb=" O ASP K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 306 Processing helix chain 'K' and resid 309 through 314 removed outlier: 3.633A pdb=" N SER K 314 " --> pdb=" O TYR K 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 24 Processing helix chain 'L' and resid 62 through 80 Processing helix chain 'L' and resid 107 through 120 Processing helix chain 'L' and resid 131 through 138 Processing helix chain 'L' and resid 147 through 159 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'L' and resid 174 through 186 Processing helix chain 'L' and resid 226 through 239 Processing helix chain 'L' and resid 256 through 264 Processing helix chain 'L' and resid 277 through 284 removed outlier: 3.668A pdb=" N HIS L 283 " --> pdb=" O ASP L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 306 Processing helix chain 'L' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER L 314 " --> pdb=" O TYR L 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS A 5 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL A 56 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE A 7 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A 88 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS A 123 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET A 127 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 124 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU A 145 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR A 126 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 208 removed outlier: 6.697A pdb=" N MET A 222 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY A 251 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 268 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS A 250 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS B 5 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL B 56 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE B 7 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL B 53 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL B 88 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS B 123 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET B 127 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 124 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU B 145 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR B 126 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA6, first strand: chain 'B' and resid 205 through 208 removed outlier: 6.697A pdb=" N MET B 222 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY B 251 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS B 250 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS C 5 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL C 56 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE C 7 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL C 88 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS C 123 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET C 127 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE C 124 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU C 145 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR C 126 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 30 through 34 Processing sheet with id=AA9, first strand: chain 'C' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET C 222 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY C 251 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA C 268 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS C 250 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS D 5 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL D 56 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE D 7 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL D 88 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS D 123 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET D 127 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE D 124 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU D 145 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AB3, first strand: chain 'D' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET D 222 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY D 251 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA D 268 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS D 250 " --> pdb=" O THR D 272 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS E 5 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL E 56 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE E 7 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL E 53 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL E 88 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE E 55 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS E 123 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET E 127 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE E 124 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU E 145 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR E 126 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 34 Processing sheet with id=AB6, first strand: chain 'E' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET E 222 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY E 251 " --> pdb=" O MET E 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N HIS E 250 " --> pdb=" O THR E 272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS F 5 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL F 56 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE F 7 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL F 53 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL F 88 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE F 55 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS F 123 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET F 127 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE F 124 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU F 145 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR F 126 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 30 through 34 Processing sheet with id=AB9, first strand: chain 'F' and resid 205 through 208 removed outlier: 6.697A pdb=" N MET F 222 " --> pdb=" O THR F 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY F 251 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS F 250 " --> pdb=" O THR F 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS G 5 " --> pdb=" O TYR G 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL G 56 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE G 7 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL G 53 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL G 88 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE G 55 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS G 123 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET G 127 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE G 124 " --> pdb=" O ASP G 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU G 145 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR G 126 " --> pdb=" O LEU G 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 30 through 34 Processing sheet with id=AC3, first strand: chain 'G' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET G 222 " --> pdb=" O THR G 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY G 251 " --> pdb=" O MET G 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA G 268 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS G 250 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS H 5 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL H 56 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE H 7 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL H 53 " --> pdb=" O THR H 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL H 88 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE H 55 " --> pdb=" O VAL H 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS H 123 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET H 127 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE H 124 " --> pdb=" O ASP H 143 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU H 145 " --> pdb=" O ILE H 124 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR H 126 " --> pdb=" O LEU H 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 30 through 34 Processing sheet with id=AC6, first strand: chain 'H' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET H 222 " --> pdb=" O THR H 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY H 251 " --> pdb=" O MET H 222 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA H 268 " --> pdb=" O VAL H 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS H 250 " --> pdb=" O THR H 272 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS I 5 " --> pdb=" O TYR I 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL I 56 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE I 7 " --> pdb=" O VAL I 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL I 53 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL I 88 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE I 55 " --> pdb=" O VAL I 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS I 123 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET I 127 " --> pdb=" O ILE I 89 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE I 124 " --> pdb=" O ASP I 143 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU I 145 " --> pdb=" O ILE I 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR I 126 " --> pdb=" O LEU I 145 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 30 through 34 Processing sheet with id=AC9, first strand: chain 'I' and resid 205 through 208 removed outlier: 6.697A pdb=" N MET I 222 " --> pdb=" O THR I 249 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY I 251 " --> pdb=" O MET I 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA I 268 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS I 250 " --> pdb=" O THR I 272 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS J 5 " --> pdb=" O TYR J 54 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL J 56 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE J 7 " --> pdb=" O VAL J 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL J 53 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL J 88 " --> pdb=" O VAL J 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE J 55 " --> pdb=" O VAL J 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS J 123 " --> pdb=" O VAL J 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET J 127 " --> pdb=" O ILE J 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE J 124 " --> pdb=" O ASP J 143 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU J 145 " --> pdb=" O ILE J 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR J 126 " --> pdb=" O LEU J 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 30 through 34 Processing sheet with id=AD3, first strand: chain 'J' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET J 222 " --> pdb=" O THR J 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY J 251 " --> pdb=" O MET J 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA J 268 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS J 250 " --> pdb=" O THR J 272 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS K 5 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL K 56 " --> pdb=" O LYS K 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE K 7 " --> pdb=" O VAL K 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL K 53 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL K 88 " --> pdb=" O VAL K 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE K 55 " --> pdb=" O VAL K 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS K 123 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET K 127 " --> pdb=" O ILE K 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE K 124 " --> pdb=" O ASP K 143 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU K 145 " --> pdb=" O ILE K 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR K 126 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 30 through 34 Processing sheet with id=AD6, first strand: chain 'K' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET K 222 " --> pdb=" O THR K 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY K 251 " --> pdb=" O MET K 222 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA K 268 " --> pdb=" O VAL K 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS K 250 " --> pdb=" O THR K 272 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS L 5 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL L 56 " --> pdb=" O LYS L 5 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE L 7 " --> pdb=" O VAL L 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL L 53 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL L 88 " --> pdb=" O VAL L 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE L 55 " --> pdb=" O VAL L 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS L 123 " --> pdb=" O VAL L 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET L 127 " --> pdb=" O ILE L 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE L 124 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU L 145 " --> pdb=" O ILE L 124 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR L 126 " --> pdb=" O LEU L 145 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 30 through 34 Processing sheet with id=AD9, first strand: chain 'L' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET L 222 " --> pdb=" O THR L 249 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY L 251 " --> pdb=" O MET L 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA L 268 " --> pdb=" O VAL L 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS L 250 " --> pdb=" O THR L 272 " (cutoff:3.500A) 1428 hydrogen bonds defined for protein. 3996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.65 Time building geometry restraints manager: 8.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9333 1.33 - 1.45: 3391 1.45 - 1.57: 16172 1.57 - 1.69: 60 1.69 - 1.81: 300 Bond restraints: 29256 Sorted by residual: bond pdb=" O4 PO4 A 403 " pdb=" P PO4 A 403 " ideal model delta sigma weight residual 1.568 1.497 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O4 PO4 G 403 " pdb=" P PO4 G 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O4 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" O4 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" O4 PO4 K 403 " pdb=" P PO4 K 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 29251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 38097 1.51 - 3.01: 1273 3.01 - 4.52: 242 4.52 - 6.03: 48 6.03 - 7.54: 12 Bond angle restraints: 39672 Sorted by residual: angle pdb=" PB ATP L 401 " pdb=" O3B ATP L 401 " pdb=" PG ATP L 401 " ideal model delta sigma weight residual 139.87 132.33 7.54 1.00e+00 1.00e+00 5.68e+01 angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 132.34 7.53 1.00e+00 1.00e+00 5.66e+01 angle pdb=" PB ATP I 401 " pdb=" O3B ATP I 401 " pdb=" PG ATP I 401 " ideal model delta sigma weight residual 139.87 132.37 7.50 1.00e+00 1.00e+00 5.62e+01 angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 132.38 7.49 1.00e+00 1.00e+00 5.61e+01 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 132.39 7.48 1.00e+00 1.00e+00 5.59e+01 ... (remaining 39667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16036 17.95 - 35.90: 1352 35.90 - 53.85: 432 53.85 - 71.80: 138 71.80 - 89.75: 90 Dihedral angle restraints: 18048 sinusoidal: 7296 harmonic: 10752 Sorted by residual: dihedral pdb=" CA SER K 8 " pdb=" C SER K 8 " pdb=" N GLY K 9 " pdb=" CA GLY K 9 " ideal model delta harmonic sigma weight residual 180.00 160.62 19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER J 8 " pdb=" C SER J 8 " pdb=" N GLY J 9 " pdb=" CA GLY J 9 " ideal model delta harmonic sigma weight residual 180.00 160.62 19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER D 8 " pdb=" C SER D 8 " pdb=" N GLY D 9 " pdb=" CA GLY D 9 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 18045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2634 0.040 - 0.080: 1417 0.080 - 0.120: 489 0.120 - 0.160: 84 0.160 - 0.200: 44 Chirality restraints: 4668 Sorted by residual: chirality pdb=" CG LEU J 248 " pdb=" CB LEU J 248 " pdb=" CD1 LEU J 248 " pdb=" CD2 LEU J 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CG LEU H 248 " pdb=" CB LEU H 248 " pdb=" CD1 LEU H 248 " pdb=" CD2 LEU H 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CG LEU D 248 " pdb=" CB LEU D 248 " pdb=" CD1 LEU D 248 " pdb=" CD2 LEU D 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.69e-01 ... (remaining 4665 not shown) Planarity restraints: 5004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER I 180 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C SER I 180 " -0.030 2.00e-02 2.50e+03 pdb=" O SER I 180 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE I 181 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 180 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C SER F 180 " 0.030 2.00e-02 2.50e+03 pdb=" O SER F 180 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE F 181 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 180 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C SER L 180 " 0.029 2.00e-02 2.50e+03 pdb=" O SER L 180 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE L 181 " -0.010 2.00e-02 2.50e+03 ... (remaining 5001 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 224 2.55 - 3.13: 23022 3.13 - 3.72: 47364 3.72 - 4.31: 66713 4.31 - 4.90: 111238 Nonbonded interactions: 248561 Sorted by model distance: nonbonded pdb="MG MG D 404 " pdb=" O HOH D 501 " model vdw 1.957 2.170 nonbonded pdb="MG MG J 404 " pdb=" O HOH J 501 " model vdw 1.958 2.170 nonbonded pdb="MG MG F 404 " pdb=" O HOH F 501 " model vdw 1.958 2.170 nonbonded pdb="MG MG I 404 " pdb=" O HOH I 501 " model vdw 1.958 2.170 nonbonded pdb="MG MG B 404 " pdb=" O HOH B 501 " model vdw 1.958 2.170 ... (remaining 248556 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.28 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=0.91 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.150 Set scattering table: 0.250 Process input model: 61.620 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 29256 Z= 0.322 Angle : 0.694 7.536 39672 Z= 0.437 Chirality : 0.054 0.200 4668 Planarity : 0.003 0.019 5004 Dihedral : 17.531 89.747 11040 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.94 % Allowed : 12.56 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3660 helix: 1.27 (0.14), residues: 1488 sheet: 0.06 (0.17), residues: 948 loop : -0.38 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP E 162 HIS 0.005 0.001 HIS H 130 PHE 0.012 0.002 PHE J 189 TYR 0.023 0.004 TYR D 146 ARG 0.004 0.001 ARG F 177 Details of bonding type rmsd hydrogen bonds : bond 0.13188 ( 1428) hydrogen bonds : angle 6.05788 ( 3996) covalent geometry : bond 0.00687 (29256) covalent geometry : angle 0.69380 (39672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 713 time to evaluate : 3.131 Fit side-chains REVERT: A 29 LYS cc_start: 0.8257 (mttp) cc_final: 0.8042 (mttm) REVERT: B 294 MET cc_start: 0.8204 (pmm) cc_final: 0.7846 (pmm) REVERT: B 298 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7945 (mm-30) REVERT: C 68 MET cc_start: 0.8302 (tpp) cc_final: 0.8098 (mmm) REVERT: D 281 MET cc_start: 0.6999 (mtp) cc_final: 0.6575 (mtm) REVERT: E 29 LYS cc_start: 0.8144 (mttp) cc_final: 0.7888 (mttm) REVERT: E 51 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7671 (mm-30) REVERT: F 51 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7787 (mm-30) REVERT: F 221 ASP cc_start: 0.7814 (p0) cc_final: 0.7448 (p0) REVERT: F 248 LEU cc_start: 0.8548 (mp) cc_final: 0.8335 (mm) REVERT: G 51 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7800 (mm-30) REVERT: G 221 ASP cc_start: 0.7816 (p0) cc_final: 0.7452 (p0) REVERT: H 29 LYS cc_start: 0.8150 (mttp) cc_final: 0.7884 (mttm) REVERT: H 51 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7676 (mm-30) REVERT: I 281 MET cc_start: 0.7010 (mtp) cc_final: 0.6587 (mtm) REVERT: J 29 LYS cc_start: 0.8162 (mttp) cc_final: 0.7831 (mttm) REVERT: J 46 GLU cc_start: 0.8360 (pt0) cc_final: 0.8157 (pt0) REVERT: K 294 MET cc_start: 0.8213 (pmm) cc_final: 0.7849 (pmm) REVERT: K 298 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7942 (mm-30) REVERT: L 29 LYS cc_start: 0.8271 (mttp) cc_final: 0.8043 (mttm) outliers start: 61 outliers final: 26 residues processed: 761 average time/residue: 1.2318 time to fit residues: 1110.4146 Evaluate side-chains 605 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 579 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 314 SER Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 314 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.0060 chunk 272 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 184 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 326 optimal weight: 2.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN B 263 ASN B 288 GLN C 135 GLN D 288 GLN E 135 GLN F 288 GLN G 288 GLN H 135 GLN I 288 GLN J 135 GLN K 263 ASN K 288 GLN L 38 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.155553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.121833 restraints weight = 24489.264| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.07 r_work: 0.3201 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 648 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29256 Z= 0.140 Angle : 0.535 6.803 39672 Z= 0.303 Chirality : 0.048 0.170 4668 Planarity : 0.003 0.024 5004 Dihedral : 12.808 88.138 4360 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.74 % Allowed : 13.55 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3660 helix: 1.50 (0.14), residues: 1512 sheet: -0.01 (0.17), residues: 1008 loop : -0.19 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 162 HIS 0.005 0.001 HIS E 130 PHE 0.010 0.002 PHE B 138 TYR 0.015 0.002 TYR D 146 ARG 0.004 0.000 ARG K 163 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 1428) hydrogen bonds : angle 5.05172 ( 3996) covalent geometry : bond 0.00295 (29256) covalent geometry : angle 0.53524 (39672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 629 time to evaluate : 3.181 Fit side-chains REVERT: A 188 ASP cc_start: 0.7968 (m-30) cc_final: 0.7561 (m-30) REVERT: B 248 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8299 (mm) REVERT: B 294 MET cc_start: 0.8473 (pmm) cc_final: 0.8146 (pmm) REVERT: D 281 MET cc_start: 0.8600 (mtp) cc_final: 0.8391 (mtm) REVERT: E 51 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8044 (mm-30) REVERT: E 294 MET cc_start: 0.9011 (pmm) cc_final: 0.8716 (pmm) REVERT: F 51 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8231 (mm-30) REVERT: F 221 ASP cc_start: 0.7932 (p0) cc_final: 0.7717 (p0) REVERT: G 51 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8220 (mm-30) REVERT: G 221 ASP cc_start: 0.7946 (p0) cc_final: 0.7731 (p0) REVERT: H 51 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8048 (mm-30) REVERT: H 294 MET cc_start: 0.9013 (pmm) cc_final: 0.8717 (pmm) REVERT: I 281 MET cc_start: 0.8575 (mtp) cc_final: 0.8365 (mtm) REVERT: K 248 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8300 (mm) REVERT: K 294 MET cc_start: 0.8481 (pmm) cc_final: 0.8148 (pmm) REVERT: L 188 ASP cc_start: 0.7974 (m-30) cc_final: 0.7572 (m-30) outliers start: 86 outliers final: 41 residues processed: 665 average time/residue: 1.3606 time to fit residues: 1058.8575 Evaluate side-chains 632 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 589 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 12 HIS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 12 HIS Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 143 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 340 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 334 optimal weight: 2.9990 chunk 355 optimal weight: 4.9990 chunk 293 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS A 288 GLN B 263 ASN C 38 GLN C 123 HIS D 17 GLN D 288 GLN D 305 ASN E 123 HIS F 17 GLN F 123 HIS F 263 ASN F 288 GLN G 17 GLN G 123 HIS G 263 ASN G 288 GLN H 123 HIS I 17 GLN I 288 GLN I 305 ASN J 123 HIS K 263 ASN L 123 HIS L 288 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.137549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.102580 restraints weight = 24492.559| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.04 r_work: 0.2915 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29256 Z= 0.155 Angle : 0.545 7.062 39672 Z= 0.309 Chirality : 0.049 0.196 4668 Planarity : 0.003 0.027 5004 Dihedral : 11.689 82.632 4338 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.80 % Allowed : 13.36 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.14), residues: 3660 helix: 1.64 (0.14), residues: 1512 sheet: 0.03 (0.17), residues: 972 loop : -0.35 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 162 HIS 0.006 0.001 HIS C 130 PHE 0.010 0.002 PHE D 138 TYR 0.015 0.002 TYR E 146 ARG 0.005 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.04982 ( 1428) hydrogen bonds : angle 4.95351 ( 3996) covalent geometry : bond 0.00337 (29256) covalent geometry : angle 0.54461 (39672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 607 time to evaluate : 3.064 Fit side-chains REVERT: A 188 ASP cc_start: 0.7879 (m-30) cc_final: 0.7440 (m-30) REVERT: B 294 MET cc_start: 0.8445 (pmm) cc_final: 0.8078 (pmm) REVERT: E 51 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8016 (mm-30) REVERT: E 294 MET cc_start: 0.9023 (pmm) cc_final: 0.8740 (pmm) REVERT: F 51 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8274 (mm-30) REVERT: F 248 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8356 (mm) REVERT: G 51 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8226 (mm-30) REVERT: H 51 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8016 (mm-30) REVERT: H 294 MET cc_start: 0.9025 (pmm) cc_final: 0.8744 (pmm) REVERT: J 17 GLN cc_start: 0.9085 (tp40) cc_final: 0.8828 (tp40) REVERT: K 294 MET cc_start: 0.8443 (pmm) cc_final: 0.8072 (pmm) REVERT: L 188 ASP cc_start: 0.7862 (m-30) cc_final: 0.7421 (m-30) outliers start: 88 outliers final: 48 residues processed: 647 average time/residue: 1.2914 time to fit residues: 985.0429 Evaluate side-chains 647 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 598 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain G residue 12 HIS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 151 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 253 optimal weight: 0.5980 chunk 290 optimal weight: 7.9990 chunk 306 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 276 optimal weight: 0.7980 chunk 315 optimal weight: 1.9990 chunk 49 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 263 ASN F 263 ASN F 288 GLN G 263 ASN G 288 GLN K 263 ASN L 288 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.107125 restraints weight = 24933.031| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.05 r_work: 0.2969 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 29256 Z= 0.108 Angle : 0.481 5.481 39672 Z= 0.272 Chirality : 0.047 0.187 4668 Planarity : 0.003 0.025 5004 Dihedral : 10.632 77.230 4338 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.13 % Allowed : 14.25 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.14), residues: 3660 helix: 1.79 (0.14), residues: 1512 sheet: -0.14 (0.16), residues: 1008 loop : -0.21 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 162 HIS 0.003 0.001 HIS G 12 PHE 0.008 0.001 PHE D 138 TYR 0.012 0.001 TYR J 146 ARG 0.006 0.000 ARG I 22 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 1428) hydrogen bonds : angle 4.79751 ( 3996) covalent geometry : bond 0.00219 (29256) covalent geometry : angle 0.48096 (39672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 612 time to evaluate : 3.379 Fit side-chains REVERT: A 188 ASP cc_start: 0.7769 (m-30) cc_final: 0.7310 (m-30) REVERT: B 205 MET cc_start: 0.7794 (mtt) cc_final: 0.7561 (mtt) REVERT: B 294 MET cc_start: 0.8458 (pmm) cc_final: 0.8079 (pmm) REVERT: C 14 ASP cc_start: 0.8506 (t70) cc_final: 0.8290 (t0) REVERT: D 17 GLN cc_start: 0.9058 (tp-100) cc_final: 0.8819 (tp-100) REVERT: E 51 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7975 (mm-30) REVERT: E 294 MET cc_start: 0.9001 (pmm) cc_final: 0.8718 (pmm) REVERT: F 51 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8212 (mm-30) REVERT: F 181 ILE cc_start: 0.8469 (mt) cc_final: 0.8267 (mt) REVERT: F 248 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8367 (mm) REVERT: G 51 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8205 (mm-30) REVERT: G 181 ILE cc_start: 0.8476 (mt) cc_final: 0.8272 (mt) REVERT: H 51 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7975 (mm-30) REVERT: H 294 MET cc_start: 0.8993 (pmm) cc_final: 0.8709 (pmm) REVERT: I 17 GLN cc_start: 0.9070 (tp-100) cc_final: 0.8827 (tp-100) REVERT: J 14 ASP cc_start: 0.8497 (t70) cc_final: 0.8260 (t0) REVERT: K 205 MET cc_start: 0.7792 (mtt) cc_final: 0.7553 (mtt) REVERT: K 294 MET cc_start: 0.8453 (pmm) cc_final: 0.8074 (pmm) REVERT: L 188 ASP cc_start: 0.7751 (m-30) cc_final: 0.7290 (m-30) outliers start: 67 outliers final: 40 residues processed: 648 average time/residue: 1.3424 time to fit residues: 1021.9449 Evaluate side-chains 613 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 572 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 300 optimal weight: 6.9990 chunk 339 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 193 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 HIS B 263 ASN B 288 GLN C 38 GLN D 123 HIS F 17 GLN F 263 ASN F 288 GLN G 17 GLN G 263 ASN G 288 GLN I 123 HIS J 38 GLN K 123 HIS K 263 ASN K 288 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.138297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.102289 restraints weight = 24529.678| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.07 r_work: 0.2936 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29256 Z= 0.155 Angle : 0.531 6.541 39672 Z= 0.300 Chirality : 0.049 0.185 4668 Planarity : 0.003 0.026 5004 Dihedral : 11.165 81.868 4338 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.10 % Allowed : 14.63 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.14), residues: 3660 helix: 1.79 (0.14), residues: 1512 sheet: 0.02 (0.17), residues: 912 loop : -0.34 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 162 HIS 0.005 0.001 HIS H 130 PHE 0.009 0.002 PHE D 138 TYR 0.016 0.002 TYR J 146 ARG 0.005 0.000 ARG K 163 Details of bonding type rmsd hydrogen bonds : bond 0.04800 ( 1428) hydrogen bonds : angle 4.83199 ( 3996) covalent geometry : bond 0.00338 (29256) covalent geometry : angle 0.53127 (39672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 585 time to evaluate : 3.257 Fit side-chains REVERT: B 39 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: B 205 MET cc_start: 0.7862 (mtt) cc_final: 0.7626 (mtt) REVERT: B 294 MET cc_start: 0.8462 (pmm) cc_final: 0.8074 (pmm) REVERT: E 294 MET cc_start: 0.9026 (pmm) cc_final: 0.8719 (pmm) REVERT: F 51 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8206 (mm-30) REVERT: F 69 GLU cc_start: 0.8991 (tt0) cc_final: 0.8660 (tt0) REVERT: F 248 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8369 (mm) REVERT: G 51 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8202 (mm-30) REVERT: G 69 GLU cc_start: 0.8981 (tt0) cc_final: 0.8693 (tt0) REVERT: H 294 MET cc_start: 0.9028 (pmm) cc_final: 0.8723 (pmm) REVERT: K 39 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8345 (mt-10) REVERT: K 205 MET cc_start: 0.7859 (mtt) cc_final: 0.7617 (mtt) REVERT: K 294 MET cc_start: 0.8460 (pmm) cc_final: 0.8069 (pmm) outliers start: 66 outliers final: 48 residues processed: 611 average time/residue: 1.2913 time to fit residues: 929.7129 Evaluate side-chains 622 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 571 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 205 MET Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 205 MET Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 128 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 226 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 284 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 188 optimal weight: 9.9990 chunk 199 optimal weight: 0.1980 chunk 138 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN F 263 ASN F 288 GLN G 263 ASN G 288 GLN K 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.141399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105587 restraints weight = 24712.850| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.07 r_work: 0.2965 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 29256 Z= 0.110 Angle : 0.480 5.329 39672 Z= 0.270 Chirality : 0.047 0.194 4668 Planarity : 0.003 0.023 5004 Dihedral : 10.350 77.116 4337 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.94 % Allowed : 15.24 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.14), residues: 3660 helix: 1.87 (0.14), residues: 1512 sheet: -0.20 (0.16), residues: 1008 loop : -0.19 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 162 HIS 0.003 0.001 HIS C 130 PHE 0.008 0.001 PHE D 138 TYR 0.013 0.001 TYR C 146 ARG 0.005 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 1428) hydrogen bonds : angle 4.70994 ( 3996) covalent geometry : bond 0.00227 (29256) covalent geometry : angle 0.48025 (39672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 591 time to evaluate : 3.030 Fit side-chains REVERT: B 205 MET cc_start: 0.7828 (mtt) cc_final: 0.7618 (mtt) REVERT: B 294 MET cc_start: 0.8469 (pmm) cc_final: 0.8092 (pmm) REVERT: C 14 ASP cc_start: 0.8520 (t70) cc_final: 0.8289 (t0) REVERT: D 17 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8781 (tp-100) REVERT: E 294 MET cc_start: 0.9005 (pmm) cc_final: 0.8718 (pmm) REVERT: F 51 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8175 (mm-30) REVERT: F 69 GLU cc_start: 0.8993 (tt0) cc_final: 0.8703 (tt0) REVERT: F 248 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8379 (mm) REVERT: G 51 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8199 (mm-30) REVERT: G 69 GLU cc_start: 0.8968 (tt0) cc_final: 0.8657 (tt0) REVERT: H 294 MET cc_start: 0.9000 (pmm) cc_final: 0.8714 (pmm) REVERT: I 17 GLN cc_start: 0.9078 (tp-100) cc_final: 0.8794 (tp-100) REVERT: J 14 ASP cc_start: 0.8533 (t70) cc_final: 0.8289 (t0) REVERT: K 205 MET cc_start: 0.7835 (mtt) cc_final: 0.7623 (mtt) REVERT: K 294 MET cc_start: 0.8465 (pmm) cc_final: 0.8081 (pmm) outliers start: 61 outliers final: 36 residues processed: 621 average time/residue: 1.3281 time to fit residues: 966.6441 Evaluate side-chains 612 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 575 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 205 MET Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 257 optimal weight: 10.0000 chunk 172 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 296 optimal weight: 0.9990 chunk 317 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 315 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN C 38 GLN F 263 ASN F 288 GLN G 263 ASN G 288 GLN K 263 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.102613 restraints weight = 24570.689| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.09 r_work: 0.2966 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29256 Z= 0.130 Angle : 0.502 5.620 39672 Z= 0.283 Chirality : 0.048 0.186 4668 Planarity : 0.003 0.022 5004 Dihedral : 10.529 78.523 4336 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.88 % Allowed : 15.43 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.14), residues: 3660 helix: 1.86 (0.14), residues: 1512 sheet: -0.21 (0.16), residues: 1008 loop : -0.19 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 162 HIS 0.004 0.001 HIS H 130 PHE 0.008 0.001 PHE I 138 TYR 0.014 0.002 TYR F 311 ARG 0.004 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 1428) hydrogen bonds : angle 4.71479 ( 3996) covalent geometry : bond 0.00278 (29256) covalent geometry : angle 0.50169 (39672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 571 time to evaluate : 3.068 Fit side-chains REVERT: B 69 GLU cc_start: 0.9063 (tt0) cc_final: 0.8746 (tt0) REVERT: B 294 MET cc_start: 0.8464 (pmm) cc_final: 0.8068 (pmm) REVERT: C 286 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8316 (ptmt) REVERT: D 17 GLN cc_start: 0.9079 (tp-100) cc_final: 0.8838 (tp-100) REVERT: D 248 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8315 (mm) REVERT: E 180 SER cc_start: 0.8711 (t) cc_final: 0.8482 (t) REVERT: E 294 MET cc_start: 0.8996 (pmm) cc_final: 0.8692 (pmm) REVERT: F 51 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8157 (mm-30) REVERT: F 69 GLU cc_start: 0.9007 (tt0) cc_final: 0.8799 (tt0) REVERT: F 224 ASP cc_start: 0.8288 (t0) cc_final: 0.7995 (t0) REVERT: F 248 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8361 (mm) REVERT: G 51 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8156 (mm-30) REVERT: G 69 GLU cc_start: 0.8969 (tt0) cc_final: 0.8767 (tt0) REVERT: G 224 ASP cc_start: 0.8252 (t0) cc_final: 0.7945 (t0) REVERT: G 248 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8371 (mm) REVERT: H 294 MET cc_start: 0.8995 (pmm) cc_final: 0.8692 (pmm) REVERT: I 17 GLN cc_start: 0.9084 (tp-100) cc_final: 0.8844 (tp-100) REVERT: I 248 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8321 (mm) REVERT: J 286 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8321 (ptmt) REVERT: K 294 MET cc_start: 0.8466 (pmm) cc_final: 0.8067 (pmm) outliers start: 59 outliers final: 40 residues processed: 600 average time/residue: 1.3278 time to fit residues: 934.1558 Evaluate side-chains 613 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 567 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 286 LYS Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 205 MET Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 193 optimal weight: 0.6980 chunk 143 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 263 optimal weight: 4.9990 chunk 250 optimal weight: 8.9990 chunk 288 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 265 optimal weight: 0.9980 chunk 218 optimal weight: 8.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 HIS B 263 ASN B 288 GLN C 38 GLN D 12 HIS F 17 GLN F 263 ASN F 288 GLN G 17 GLN G 263 ASN G 288 GLN I 12 HIS J 38 GLN K 12 HIS K 263 ASN K 288 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.098388 restraints weight = 24537.152| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.09 r_work: 0.2869 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 29256 Z= 0.265 Angle : 0.629 7.497 39672 Z= 0.354 Chirality : 0.054 0.237 4668 Planarity : 0.004 0.038 5004 Dihedral : 12.430 87.210 4336 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.04 % Allowed : 15.17 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 3660 helix: 1.62 (0.14), residues: 1512 sheet: 0.15 (0.16), residues: 948 loop : -0.51 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP L 162 HIS 0.008 0.001 HIS A 130 PHE 0.010 0.002 PHE B 189 TYR 0.024 0.003 TYR C 146 ARG 0.006 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.05847 ( 1428) hydrogen bonds : angle 4.98611 ( 3996) covalent geometry : bond 0.00609 (29256) covalent geometry : angle 0.62870 (39672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 609 time to evaluate : 2.983 Fit side-chains REVERT: A 188 ASP cc_start: 0.7850 (m-30) cc_final: 0.7554 (m-30) REVERT: B 294 MET cc_start: 0.8445 (pmm) cc_final: 0.8039 (pmm) REVERT: C 286 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8378 (ptmt) REVERT: D 17 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8795 (tp-100) REVERT: D 281 MET cc_start: 0.8659 (mtm) cc_final: 0.8458 (mtp) REVERT: E 294 MET cc_start: 0.9011 (pmm) cc_final: 0.8679 (pmm) REVERT: F 51 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8261 (mm-30) REVERT: F 163 ARG cc_start: 0.8550 (mtt90) cc_final: 0.8341 (mtt180) REVERT: G 51 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8263 (mm-30) REVERT: G 163 ARG cc_start: 0.8547 (mtt90) cc_final: 0.8339 (mtt180) REVERT: H 294 MET cc_start: 0.9012 (pmm) cc_final: 0.8680 (pmm) REVERT: I 17 GLN cc_start: 0.9060 (tp-100) cc_final: 0.8764 (tp-100) REVERT: J 286 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8381 (ptmt) REVERT: K 294 MET cc_start: 0.8442 (pmm) cc_final: 0.8034 (pmm) REVERT: L 188 ASP cc_start: 0.7860 (m-30) cc_final: 0.7568 (m-30) outliers start: 64 outliers final: 43 residues processed: 633 average time/residue: 1.4036 time to fit residues: 1035.7688 Evaluate side-chains 631 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 586 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 286 LYS Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 205 MET Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 258 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 309 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 237 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN B 288 GLN C 38 GLN F 288 GLN G 288 GLN I 17 GLN K 263 ASN K 288 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.101334 restraints weight = 24613.129| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.19 r_work: 0.2924 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29256 Z= 0.144 Angle : 0.530 6.320 39672 Z= 0.298 Chirality : 0.049 0.231 4668 Planarity : 0.003 0.027 5004 Dihedral : 11.338 84.896 4336 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.53 % Allowed : 15.62 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 3660 helix: 1.72 (0.14), residues: 1512 sheet: -0.13 (0.16), residues: 1008 loop : -0.29 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 162 HIS 0.005 0.001 HIS H 130 PHE 0.009 0.001 PHE B 138 TYR 0.017 0.002 TYR C 146 ARG 0.006 0.000 ARG K 163 Details of bonding type rmsd hydrogen bonds : bond 0.04644 ( 1428) hydrogen bonds : angle 4.81221 ( 3996) covalent geometry : bond 0.00310 (29256) covalent geometry : angle 0.52985 (39672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 581 time to evaluate : 3.241 Fit side-chains REVERT: B 69 GLU cc_start: 0.9131 (tt0) cc_final: 0.8802 (tt0) REVERT: B 294 MET cc_start: 0.8484 (pmm) cc_final: 0.8087 (pmm) REVERT: C 286 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8319 (ptmt) REVERT: D 17 GLN cc_start: 0.9080 (tp-100) cc_final: 0.8812 (tp-100) REVERT: D 281 MET cc_start: 0.8641 (mtm) cc_final: 0.8423 (mtp) REVERT: E 294 MET cc_start: 0.9006 (pmm) cc_final: 0.8706 (pmm) REVERT: F 51 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8228 (mm-30) REVERT: F 69 GLU cc_start: 0.9051 (tt0) cc_final: 0.8696 (tt0) REVERT: F 248 LEU cc_start: 0.8657 (mt) cc_final: 0.8342 (mm) REVERT: G 51 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8240 (mm-30) REVERT: G 69 GLU cc_start: 0.9001 (tt0) cc_final: 0.8743 (tt0) REVERT: G 248 LEU cc_start: 0.8659 (mt) cc_final: 0.8338 (mm) REVERT: H 294 MET cc_start: 0.9007 (pmm) cc_final: 0.8709 (pmm) REVERT: J 286 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8315 (ptmt) REVERT: K 69 GLU cc_start: 0.9047 (tt0) cc_final: 0.8834 (tt0) REVERT: K 294 MET cc_start: 0.8479 (pmm) cc_final: 0.8074 (pmm) outliers start: 48 outliers final: 35 residues processed: 606 average time/residue: 1.3647 time to fit residues: 965.1032 Evaluate side-chains 602 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 565 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 286 LYS Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 205 MET Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 187 optimal weight: 2.9990 chunk 317 optimal weight: 10.0000 chunk 228 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 274 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN B 288 GLN C 38 GLN F 288 GLN G 263 ASN G 288 GLN J 38 GLN K 263 ASN K 288 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.100620 restraints weight = 24555.417| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.10 r_work: 0.2901 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 29256 Z= 0.170 Angle : 0.558 6.757 39672 Z= 0.314 Chirality : 0.050 0.223 4668 Planarity : 0.003 0.030 5004 Dihedral : 11.579 87.037 4334 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.43 % Allowed : 16.22 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.14), residues: 3660 helix: 1.68 (0.14), residues: 1512 sheet: -0.10 (0.16), residues: 972 loop : -0.42 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 162 HIS 0.005 0.001 HIS H 130 PHE 0.010 0.002 PHE I 138 TYR 0.020 0.002 TYR J 146 ARG 0.007 0.000 ARG F 163 Details of bonding type rmsd hydrogen bonds : bond 0.04963 ( 1428) hydrogen bonds : angle 4.84116 ( 3996) covalent geometry : bond 0.00376 (29256) covalent geometry : angle 0.55847 (39672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 577 time to evaluate : 3.325 Fit side-chains REVERT: B 69 GLU cc_start: 0.9108 (tt0) cc_final: 0.8884 (tt0) REVERT: B 294 MET cc_start: 0.8492 (pmm) cc_final: 0.8091 (pmm) REVERT: C 286 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8334 (ptmt) REVERT: D 17 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8793 (tp-100) REVERT: D 281 MET cc_start: 0.8645 (mtm) cc_final: 0.8435 (mtp) REVERT: E 294 MET cc_start: 0.8985 (pmm) cc_final: 0.8668 (pmm) REVERT: F 51 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8231 (mm-30) REVERT: F 248 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8330 (mm) REVERT: G 51 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8241 (mm-30) REVERT: G 69 GLU cc_start: 0.9006 (tt0) cc_final: 0.8759 (tt0) REVERT: G 248 LEU cc_start: 0.8674 (mt) cc_final: 0.8322 (mm) REVERT: H 294 MET cc_start: 0.8986 (pmm) cc_final: 0.8672 (pmm) REVERT: I 17 GLN cc_start: 0.9056 (tp-100) cc_final: 0.8785 (tp-100) REVERT: J 286 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8333 (ptmt) REVERT: K 294 MET cc_start: 0.8494 (pmm) cc_final: 0.8094 (pmm) outliers start: 45 outliers final: 36 residues processed: 600 average time/residue: 1.3730 time to fit residues: 959.7294 Evaluate side-chains 614 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 575 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 286 LYS Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 205 MET Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 260 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 292 optimal weight: 3.9990 chunk 267 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 249 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN B 288 GLN C 38 GLN F 288 GLN G 263 ASN G 288 GLN J 38 GLN K 263 ASN K 288 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.138081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.101705 restraints weight = 24605.028| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.09 r_work: 0.2943 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29256 Z= 0.150 Angle : 0.538 7.048 39672 Z= 0.303 Chirality : 0.049 0.230 4668 Planarity : 0.003 0.026 5004 Dihedral : 11.300 85.310 4334 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.40 % Allowed : 16.32 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.14), residues: 3660 helix: 1.71 (0.14), residues: 1512 sheet: -0.19 (0.16), residues: 1008 loop : -0.29 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 162 HIS 0.005 0.001 HIS H 130 PHE 0.010 0.001 PHE I 138 TYR 0.018 0.002 TYR C 146 ARG 0.007 0.000 ARG G 163 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 1428) hydrogen bonds : angle 4.79213 ( 3996) covalent geometry : bond 0.00328 (29256) covalent geometry : angle 0.53839 (39672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28411.02 seconds wall clock time: 487 minutes 40.60 seconds (29260.60 seconds total)